Figure 12. Regulatory evolution of paralogous genes in glucose depletion and heat shock.
(A)–(D) several regulatory fates of paralogous genes following duplication, relative to their immediate pre-duplication ancestor in each of glucose depletion and heat shock. For each condition shown are cartoon gene trees (left) and illustrative examples from our analysis (right) representing the module assignment (circles) of each paralog and their pre-duplication ortholog in each extant and ancestral species. Module assignment is color coded as in Figure 3 (Bright blue, light blue, white, pink and red from Module 1 to 5, respectively). Star: gene duplication. Lightning rod: gene loss. (A) Conserved: both paralogs (UTP5 and UTP9) conserve the ancestral assignment (Module 1) in both responses; (B) Neo-functionalized, one paralog: one paralog (URA7) maintains the ancestral assignment (Module 1) and the other (URA8) is assigned to a different module (Module 5) in both responses; (C) Neo-functionalized, both paralogs: both paralogs (POR1, POR2) are reassigned to distinct modules than the ancestral one, but in different ways in each response. (D) Sub-functionalization: In glucose depletion, one paralog (RFX1) maintains the ancestral assignment (Module 2) and the other (OG1201) is reassigned (Module 3). This pattern is reversed in heat shock. (E) Number of paralogs pairs in each of the classes.